Metagenomic Snapshots of Viral Components in Guinean Bats

Total Page:16

File Type:pdf, Size:1020Kb

Metagenomic Snapshots of Viral Components in Guinean Bats microorganisms Communication Metagenomic Snapshots of Viral Components in Guinean Bats Roberto J. Hermida Lorenzo 1,†,Dániel Cadar 2,† , Fara Raymond Koundouno 3, Javier Juste 4,5 , Alexandra Bialonski 2, Heike Baum 2, Juan Luis García-Mudarra 4, Henry Hakamaki 2, András Bencsik 2, Emily V. Nelson 2, Miles W. Carroll 6,7, N’Faly Magassouba 3, Stephan Günther 2,8, Jonas Schmidt-Chanasit 2,9 , César Muñoz Fontela 2,8 and Beatriz Escudero-Pérez 2,8,* 1 Morcegos de Galicia, Magdalena G-2, 2o izq, 15320 As Pontes de García Rodríguez (A Coruña), Spain; [email protected] 2 WHO Collaborating Centre for Arbovirus and Haemorrhagic Fever Reference and Research, Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany; [email protected] (D.C.); [email protected] (A.B.); [email protected] (H.B.); [email protected] (H.H.); [email protected] (A.B.); [email protected] (E.V.N.); [email protected] (S.G.); [email protected] (J.S.-C.); [email protected] (C.M.F.) 3 Laboratoire des Fièvres Hémorragiques en Guinée, Université Gamal Abdel Nasser de Conakry, Commune de Matoto, Conakry, Guinea; [email protected] (F.R.K.); [email protected] (N.M.) 4 Estación Biológica de Doñana, CSIC, 41092 Seville, Spain; [email protected] (J.J.); [email protected] (J.L.G.-M.) 5 CIBER Epidemiology and Public Health (CIBERESP), 28029 Madrid, Spain 6 Public Health England, Porton Down, Wiltshire SP4 0JG, UK; [email protected] 7 Wellcome Centre for Human Genetics, Nuffield Department of Medicine, Oxford University, Oxford OX3 7BN, UK Citation: Hermida Lorenzo, R.J.; 8 German Centre for Infection Research (DZIF), Partner Site Hamburg-Luebeck-Borstel, Cadar, D.; Koundouno, F.R.; Juste, J.; 38124 Braunschweig, Germany Bialonski, A.; Baum, H.; 9 Faculty of Mathematics, Informatics and Natural Sciences, Universität Hamburg, 20148 Hamburg, Germany García-Mudarra, J.L.; Hakamaki, H.; * Correspondence: [email protected] Bencsik, A.; Nelson, E.V.; et al. † These authors contributed equally to this work. Metagenomic Snapshots of Viral Components in Guinean Bats. Abstract: To prevent the emergence of zoonotic infectious diseases and reduce their epidemic Microorganisms 2021, 9, 599. potential, we need to understand their origins in nature. Bats in the order Chiroptera are widely https://doi.org/10.3390/ distributed worldwide and are natural reservoirs of prominent zoonotic viruses, including Nipah microorganisms9030599 virus, Marburg virus, and possibly SARS-CoV-2. In this study, we applied unbiased metagenomic and metatranscriptomic approaches to decipher the virosphere of frugivorous and insectivorous Academic Editor: bat species captured in Guéckédou, Guinea, the epicenter of the West African Ebola virus disease Anne Balkema-Buschmann epidemic in 2013–2016. Our study provides a snapshot of the viral diversity present in these bat species, with several novel viruses reported for the first time in bats, as well as some bat viruses closely Received: 18 February 2021 Accepted: 8 March 2021 related to known human or animal pathogens. In addition, analysis of Mops condylurus genomic DNA Published: 15 March 2021 samples revealed the presence of an Ebola virus nucleoprotein (NP)-derived pseudogene inserted in its genome. These findings provide insight into the evolutionary traits of several virus families in Publisher’s Note: MDPI stays neutral bats and add evidence that nonretroviral integrated RNA viruses (NIRVs) derived from filoviruses with regard to jurisdictional claims in may be common in bat genomes. published maps and institutional affil- iations. Keywords: bats; host; zoonosis; Ebola virus; nonretroviral integrated RNA viruses (NIRVs) Copyright: © 2021 by the authors. 1. Introduction Licensee MDPI, Basel, Switzerland. Due to their biodiversity, rainforest areas of Central and Western Africa are considered This article is an open access article hotspots for the emergence of zoonotic viruses, and a number of prominent viruses with distributed under the terms and epidemic potential have been identified in this region [1]. Approximately 75% of emerging conditions of the Creative Commons infectious diseases in humans are zoonoses [2,3]. The rate of detection of zoonotic viruses Attribution (CC BY) license (https:// has increased in past decades, possibly due to improved diagnostic capacity and surveil- creativecommons.org/licenses/by/ lance efforts [4,5]. Many novel pathogens that have caused epidemics and pandemics have 4.0/). Microorganisms 2021, 9, 599. https://doi.org/10.3390/microorganisms9030599 https://www.mdpi.com/journal/microorganisms Microorganisms 2021, 9, 599 2 of 13 emerged from bats, including Nipah virus, MERS-coronavirus, Marburg virus, and likely Ebola virus (EBOV) and SARS-CoV-2 [6]. Due to the importance of bats as virus reservoirs, it is paramount to regularly investi- gate the bat virome and to assess the potential human pathogenicity of viruses circulating in bats. In this regard, metagenomic analyses of bat viromes can provide relevant infor- mation about viruses circulating in frugivorous and insectivorous bats living in a specific area. Subsequent phylogenetic analyses can evaluate the proximity of bat viruses to known pathogenic human viruses, which may help gauge potential spillover events into humans. For instance, potential novel variants of paramyxovirus and coronaviruses have been shown to commonly circulate in bats [7,8]. In addition, metagenomic analyses of bat viromes have served, for example, to identify novel filoviruses such as Bombali virus in Mops condylurus [9] and Mengla dianlovirus in Rousettus bats [10–13], which provides evidence for bats as reservoirs for Ebola virus (EBOV). Furthermore, EBOV RNA has been detected in three fruit bat species: Epomops franqueti, Hypsignathus monstrosus, and Myonycteris torquata [14]. Anti-EBOV antibodies have been shown in those species, as well as in Eidolon helvum, Epomophorus gambianus, Micropteropus pusillus, Mops condylurus, Rousettus aegyptiacus, and Rousettus leschenaultii [15]. Finally, in silico analyses of mammalian genomes in the order Mononegavirales have identified nonretroviral sequences derived from single-strand RNA viruses (NIRVs) that are integrated into the genomes of several mammalian species, including bats. Of these, bornavirus NIRVs are the best-characterized [16,17]. Filovirus-derived pseudogenes have also been identified in the genome of bats, marsupials, and rodents [18]. These NIRVs are thought to have their origin in nonhomologous recombination events with genomic transposons during infection [19–21]. Because phylogenetic studies show that these sequences are essentially paleovirus sequences, these findings indicate that filoviruses are ancient and have a long relationship with these mammalian species. In this study, bats captured in the rainforest area of Guéckédou in the Republic of Guinea were sampled via metagenomic and metatranscriptomic studies to characterize the virome of these bat species. In addition, genomic DNA samples were also screened for the presence of possible filovirus-derived nonretroviral integrated RNA virus (NIRV) sequences. The overall goal was to gain insight into the viruses circulating in bats in the area where the 2013–2016 Ebola virus disease (EVD) epidemic started and to underscore the importance of bat surveillance to prevent potential zoonotic outbreaks. 2. Materials and Methods 2.1. Bat Capturing and Sampling The objectives of the present study were communicated to the local community leaders in the Guéckédou prefecture, as well as to the regional government. This study was approved the 7 February 2017 by the Ministère de l’Elèvage et des Productions Animals and the Direction Nationale des Services Vétérinaires de la Republique de Guinée under permit number 015/MEPA/DNSV/2016. The capture and handling of animals and samples were conducted only by trained individuals. Personal safety equipment for capture included leather gloves, goggles, and masks. Bats were sampled in eight locations in the Guéckédou prefecture over the course of five days, between 10 and 15 April 2017. Bats were captured with 9 m and 12 m mist nets at different heights in Guéckédou (Kimberlite garden), Tékoulo (Tékoulo village and Bakama Lela cave), Temessadou (Mongo forest), Nongoa (Nongoa village and Tongdou cave), and Koundou-Lengobengou (Koundou village and Koundou forest) (Figure1). Different environments were sampled: two caves, two construction sites, two secondary forest zones, and two rural core environments. A total of 82 bats were captured by mist nets and kept in cloth bags until sample collection. The forearm length and weight of each specimen were measured. Bats were released after the authors took a blood sample (for virus detection) and a patagium sample (for species identification); these were conserved in AVL and 70% ethanol, respectively. One specimen with a broken wing was euthanized under isoflurane anesthesia and cervical dislocation. Thirteen bats were Microorganisms 2021, 9, 599 3 of 13 found dead due to stress. For these 14 specimens, necropsies were performed to obtain spleen, liver, kidney, and thymus samples, which were preserved in 500 µL of RNAlater. Samples were stored initially at −20 ◦C and later at −80 ◦C. Necropsies were carried out wearing an all-over bodysuit (Tyvek), FFP3 safety mask, face shield, arm protection, and doubled gloves. All other nondisposable equipment was disinfected with 90% ethanol. Nets were dried and disinfected every morning. Bat carcasses were burned after sampling.
Recommended publications
  • Multiple Origins of Viral Capsid Proteins from Cellular Ancestors
    Multiple origins of viral capsid proteins from PNAS PLUS cellular ancestors Mart Krupovica,1 and Eugene V. Kooninb,1 aInstitut Pasteur, Department of Microbiology, Unité Biologie Moléculaire du Gène chez les Extrêmophiles, 75015 Paris, France; and bNational Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894 Contributed by Eugene V. Koonin, February 3, 2017 (sent for review December 21, 2016; reviewed by C. Martin Lawrence and Kenneth Stedman) Viruses are the most abundant biological entities on earth and show genome replication. Understanding the origin of any virus group is remarkable diversity of genome sequences, replication and expres- possible only if the provenances of both components are elucidated sion strategies, and virion structures. Evolutionary genomics of (11). Given that viral replication proteins often have no closely viruses revealed many unexpected connections but the general related homologs in known cellular organisms (6, 12), it has been scenario(s) for the evolution of the virosphere remains a matter of suggested that many of these proteins evolved in the precellular intense debate among proponents of the cellular regression, escaped world (4, 6) or in primordial, now extinct, cellular lineages (5, 10, genes, and primordial virus world hypotheses. A comprehensive 13). The ability to transfer the genetic information encased within sequence and structure analysis of major virion proteins indicates capsids—the protective proteinaceous shells that comprise the that they evolved on about 20 independent occasions, and in some of cores of virus particles (virions)—is unique to bona fide viruses and these cases likely ancestors are identifiable among the proteins of distinguishes them from other types of selfish genetic elements cellular organisms.
    [Show full text]
  • A Preliminary Study of Viral Metagenomics of French Bat Species in Contact with Humans: Identification of New Mammalian Viruses
    A preliminary study of viral metagenomics of French bat species in contact with humans: identification of new mammalian viruses. Laurent Dacheux, Minerva Cervantes-Gonzalez, Ghislaine Guigon, Jean-Michel Thiberge, Mathias Vandenbogaert, Corinne Maufrais, Valérie Caro, Hervé Bourhy To cite this version: Laurent Dacheux, Minerva Cervantes-Gonzalez, Ghislaine Guigon, Jean-Michel Thiberge, Mathias Vandenbogaert, et al.. A preliminary study of viral metagenomics of French bat species in contact with humans: identification of new mammalian viruses.. PLoS ONE, Public Library of Science, 2014, 9 (1), pp.e87194. 10.1371/journal.pone.0087194.s006. pasteur-01430485 HAL Id: pasteur-01430485 https://hal-pasteur.archives-ouvertes.fr/pasteur-01430485 Submitted on 9 Jan 2017 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution| 4.0 International License A Preliminary Study of Viral Metagenomics of French Bat Species in Contact with Humans: Identification of New Mammalian Viruses Laurent Dacheux1*, Minerva Cervantes-Gonzalez1,
    [Show full text]
  • A Novel Rhabdovirus Infecting Newly Discovered Nycteribiid Bat Flies
    www.nature.com/scientificreports OPEN Kanyawara Virus: A Novel Rhabdovirus Infecting Newly Discovered Nycteribiid Bat Flies Received: 19 April 2017 Accepted: 25 May 2017 Infesting Previously Unknown Published: xx xx xxxx Pteropodid Bats in Uganda Tony L. Goldberg 1,2,3, Andrew J. Bennett1, Robert Kityo3, Jens H. Kuhn4 & Colin A. Chapman3,5 Bats are natural reservoir hosts of highly virulent pathogens such as Marburg virus, Nipah virus, and SARS coronavirus. However, little is known about the role of bat ectoparasites in transmitting and maintaining such viruses. The intricate relationship between bats and their ectoparasites suggests that ectoparasites might serve as viral vectors, but evidence to date is scant. Bat flies, in particular, are highly specialized obligate hematophagous ectoparasites that incidentally bite humans. Using next- generation sequencing, we discovered a novel ledantevirus (mononegaviral family Rhabdoviridae, genus Ledantevirus) in nycteribiid bat flies infesting pteropodid bats in western Uganda. Mitochondrial DNA analyses revealed that both the bat flies and their bat hosts belong to putative new species. The coding-complete genome of the new virus, named Kanyawara virus (KYAV), is only distantly related to that of its closest known relative, Mount Elgon bat virus, and was found at high titers in bat flies but not in blood or on mucosal surfaces of host bats. Viral genome analysis indicates unusually low CpG dinucleotide depletion in KYAV compared to other ledanteviruses and rhabdovirus groups, with KYAV displaying values similar to rhabdoviruses of arthropods. Our findings highlight the possibility of a yet- to-be-discovered diversity of potentially pathogenic viruses in bat ectoparasites. Bats (order Chiroptera) represent the second largest order of mammals after rodents (order Rodentia).
    [Show full text]
  • Guide for Common Viral Diseases of Animals in Louisiana
    Sampling and Testing Guide for Common Viral Diseases of Animals in Louisiana Please click on the species of interest: Cattle Deer and Small Ruminants The Louisiana Animal Swine Disease Diagnostic Horses Laboratory Dogs A service unit of the LSU School of Veterinary Medicine Adapted from Murphy, F.A., et al, Veterinary Virology, 3rd ed. Cats Academic Press, 1999. Compiled by Rob Poston Multi-species: Rabiesvirus DCN LADDL Guide for Common Viral Diseases v. B2 1 Cattle Please click on the principle system involvement Generalized viral diseases Respiratory viral diseases Enteric viral diseases Reproductive/neonatal viral diseases Viral infections affecting the skin Back to the Beginning DCN LADDL Guide for Common Viral Diseases v. B2 2 Deer and Small Ruminants Please click on the principle system involvement Generalized viral disease Respiratory viral disease Enteric viral diseases Reproductive/neonatal viral diseases Viral infections affecting the skin Back to the Beginning DCN LADDL Guide for Common Viral Diseases v. B2 3 Swine Please click on the principle system involvement Generalized viral diseases Respiratory viral diseases Enteric viral diseases Reproductive/neonatal viral diseases Viral infections affecting the skin Back to the Beginning DCN LADDL Guide for Common Viral Diseases v. B2 4 Horses Please click on the principle system involvement Generalized viral diseases Neurological viral diseases Respiratory viral diseases Enteric viral diseases Abortifacient/neonatal viral diseases Viral infections affecting the skin Back to the Beginning DCN LADDL Guide for Common Viral Diseases v. B2 5 Dogs Please click on the principle system involvement Generalized viral diseases Respiratory viral diseases Enteric viral diseases Reproductive/neonatal viral diseases Back to the Beginning DCN LADDL Guide for Common Viral Diseases v.
    [Show full text]
  • Floral Biology and Pollination Strategy of Durio (Malvaceae) in Sarawak, Malaysian Borneo
    BIODIVERSITAS ISSN: 1412-033X Volume 21, Number 12, December 2020 E-ISSN: 2085-4722 Pages: 5579-5594 DOI: 10.13057/biodiv/d211203 Floral biology and pollination strategy of Durio (Malvaceae) in Sarawak, Malaysian Borneo NG WIN SENG1, JAYASILAN MOHD-AZLAN1, WONG SIN YENG1,2,♥ 1Institute of Biodiversity and Environmental Conservation, Universiti Malaysia Sarawak. 94300 Kota Samarahan, Sarawak, Malaysia. 2Harvard University Herbaria. 22 Divinity Avenue, Cambridge, MA 02138, United States of America. ♥ email: [email protected]. Manuscript received: 25 September 2020. Revision accepted: 4 November 2020. Abstract. Ng WS, Mohd-Azlan J, Wong SY. 2020. Floral biology and pollination strategy of Durio (Malvaceae) in Sarawak, Malaysian Borneo. Biodiversitas 21: 5579-5594. This study was carried out to investigate on the flowering mechanisms of four Durio species in Sarawak. The anthesis started in the afternoon (D. graveolens and D. zibethinus), evening (D. kutejensis) or midnight (D. griffithii); and lasted between 11.5 hours (D. griffithii) to 20 hours (D. graveolens). All four Durio species are generalists. Individuals of a fruit bat (Eonycteris spelaea, Pteropodidae) are considered as the main pollinator for D. graveolens, D. kutejensis, and D. zibethinus while spiderhunter (Arachnothera, Nectariniidae) is also proposed as a primary pollinator for D. kutejensis. Five invertebrate taxa were observed as secondary or inadvertent pollinators of Durio spp.: honeybee, Apis sp. (Apidae), stingless bee, Tetrigona sp. (Apidae), nocturnal wasp, Provespa sp. (Vespidae), pollen beetle (Nitidulidae), and thrip (Thysanoptera). Honey bees and stingless bees pollinated all four Durio species. Pollen beetles were found to pollinate D. griffithii and D. graveolens while nocturnal wasps were found to pollinate D.
    [Show full text]
  • Identification and Rnai Profile of a Novel Iflavirus Infecting Senegalese
    viruses Article Identification and RNAi Profile of a Novel Iflavirus Infecting Senegalese Aedes vexans arabiensis Mosquitoes 1, 2,3, 4, 5 6 Rhys Parry y , Fanny Naccache y, El Hadji Ndiaye y , Gamou Fall , Ilaria Castelli , 7,8 9,10 10, 11 Renke Lühken , Jolyon Medlock , Benjamin Cull z , Jenny C. Hesson , Fabrizio Montarsi 12, Anna-Bella Failloux 6 , Alain Kohl 13, Esther Schnettler 7,8,14, Mawlouth Diallo 4, Sassan Asgari 1, Isabelle Dietrich 15,* and Stefanie C. Becker 2,3,* 1 Australian Infectious Diseases Research Centre, School of Biological Sciences, The University of Queensland, Brisbane, QLD 4072, Australia; [email protected] (R.P.); [email protected] (S.A.) 2 Institute for Parasitology, University of Veterinary Medicine Hannover, 30559 Hannover, Germany; [email protected] 3 Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, 30559 Hannover, Germany 4 Pole de Zoologie Médicale, Institut Pasteur de Dakar, Dakar BP 220, Senegal; [email protected] (E.H.N.); [email protected] (M.D.) 5 Pole de Virologie, Unité des Arbovirus et Virus de Fièvres Hémorragiques, Institut Pasteur de Dakar, Dakar BP 220, Senegal; [email protected] 6 Arboviruses and Insect Vectors, Department of Virology, Institut Pasteur, 75724 Paris, France; [email protected] (I.C.); [email protected] (A.-B.F.) 7 Faculty of Mathematics, Informatics and Natural Sciences, Universiät Hamburg, 20148 Hamburg, Germany; [email protected] (R.L.); [email protected] (E.S.) 8 Bernhard-Nocht-Institute
    [Show full text]
  • 2020 Taxonomic Update for Phylum Negarnaviricota (Riboviria: Orthornavirae), Including the Large Orders Bunyavirales and Mononegavirales
    Archives of Virology https://doi.org/10.1007/s00705-020-04731-2 VIROLOGY DIVISION NEWS 2020 taxonomic update for phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales Jens H. Kuhn1 · Scott Adkins2 · Daniela Alioto3 · Sergey V. Alkhovsky4 · Gaya K. Amarasinghe5 · Simon J. Anthony6,7 · Tatjana Avšič‑Županc8 · María A. Ayllón9,10 · Justin Bahl11 · Anne Balkema‑Buschmann12 · Matthew J. Ballinger13 · Tomáš Bartonička14 · Christopher Basler15 · Sina Bavari16 · Martin Beer17 · Dennis A. Bente18 · Éric Bergeron19 · Brian H. Bird20 · Carol Blair21 · Kim R. Blasdell22 · Steven B. Bradfute23 · Rachel Breyta24 · Thomas Briese25 · Paul A. Brown26 · Ursula J. Buchholz27 · Michael J. Buchmeier28 · Alexander Bukreyev18,29 · Felicity Burt30 · Nihal Buzkan31 · Charles H. Calisher32 · Mengji Cao33,34 · Inmaculada Casas35 · John Chamberlain36 · Kartik Chandran37 · Rémi N. Charrel38 · Biao Chen39 · Michela Chiumenti40 · Il‑Ryong Choi41 · J. Christopher S. Clegg42 · Ian Crozier43 · John V. da Graça44 · Elena Dal Bó45 · Alberto M. R. Dávila46 · Juan Carlos de la Torre47 · Xavier de Lamballerie38 · Rik L. de Swart48 · Patrick L. Di Bello49 · Nicholas Di Paola50 · Francesco Di Serio40 · Ralf G. Dietzgen51 · Michele Digiaro52 · Valerian V. Dolja53 · Olga Dolnik54 · Michael A. Drebot55 · Jan Felix Drexler56 · Ralf Dürrwald57 · Lucie Dufkova58 · William G. Dundon59 · W. Paul Duprex60 · John M. Dye50 · Andrew J. Easton61 · Hideki Ebihara62 · Toufc Elbeaino63 · Koray Ergünay64 · Jorlan Fernandes195 · Anthony R. Fooks65 · Pierre B. H. Formenty66 · Leonie F. Forth17 · Ron A. M. Fouchier48 · Juliana Freitas‑Astúa67 · Selma Gago‑Zachert68,69 · George Fú Gāo70 · María Laura García71 · Adolfo García‑Sastre72 · Aura R. Garrison50 · Aiah Gbakima73 · Tracey Goldstein74 · Jean‑Paul J. Gonzalez75,76 · Anthony Grifths77 · Martin H. Groschup12 · Stephan Günther78 · Alexandro Guterres195 · Roy A.
    [Show full text]
  • Zoologische Mededelingen
    ZOOLOGISCHE MEDEDELINGEN UITGEGEVEN DOOR HET RIJKSMUSEUM VAN NATUURLIJKE HISTORIE TE LEIDEN (MINISTERIE VAN CULTUUR, RECREATIE EN MAATSCHAPPELIJK WERK) Deel 55 no. 14 4 maart 1980 A NEW FRUIT BAT OF THE GENUS MYONYCTERIS MATSCHIE, 1899, FROM EASTERN KENYA AND TANZANIA (MAMMALIA, MEGACHIROPTERA) by W. BERGMANS Instituut voor Taxonomische Zoölogie, Universiteit van Amsterdam With 4 text-figures ABSTRACT Myonycteris relicta n. sp. is described from the Shimba Hills in southeast Kenya and from the Usambara Mountains in northeast Tanzania. The species is larger than the only other known African mainland species of the genus, Myonycteris torquata (Dobson, 1878), from the Central and West African rain forests and, if compared to M. torquata and the only other species in the genus, M. brachycephala (Bocage, 1889) from São Tomé, has a relatively longer rostrum, a more deflected cranial axis, and further differs in number, shape and position of its teeth. The new species provides new arguments for the relationship between the genera Myonycteris Matschie, 1899, and Lissonycteris Andersen, 1912. It is believed that Myonycteris relicta may be a forest species and as such restricted to isolated East African forests. INTRODUCTION During a visit to the Zoologisches Museum in Berlin (ZMB), in April 1979, the author found two fruit bat specimens from the Tanzanian Usa- mbara Mountains, which proved to represent an undescribed taxon. Later, in June 1979, Dr C. Smeenk of the Rijksmuseum van Natuurlijke Historie at Leiden (RMNH) recognized a third specimen of this taxon in newly acquired material from the Shimba Hills in southeast Kenya. The bats differ on specific level from all other known fruit bats, and are described in the present paper.
    [Show full text]
  • And Giant Guitarfish (Rhynchobatus Djiddensis)
    VIRAL DISCOVERY IN BLUEGILL SUNFISH (LEPOMIS MACROCHIRUS) AND GIANT GUITARFISH (RHYNCHOBATUS DJIDDENSIS) BY HISTOPATHOLOGY EVALUATION, METAGENOMIC ANALYSIS AND NEXT GENERATION SEQUENCING by JENNIFER ANNE DILL (Under the Direction of Alvin Camus) ABSTRACT The rapid growth of aquaculture production and international trade in live fish has led to the emergence of many new diseases. The introduction of novel disease agents can result in significant economic losses, as well as threats to vulnerable wild fish populations. Losses are often exacerbated by a lack of agent identification, delay in the development of diagnostic tools and poor knowledge of host range and susceptibility. Examples in bluegill sunfish (Lepomis macrochirus) and the giant guitarfish (Rhynchobatus djiddensis) will be discussed here. Bluegill are popular freshwater game fish, native to eastern North America, living in shallow lakes, ponds, and slow moving waterways. Bluegill experiencing epizootics of proliferative lip and skin lesions, characterized by epidermal hyperplasia, papillomas, and rarely squamous cell carcinoma, were investigated in two isolated poopulations. Next generation genomic sequencing revealed partial DNA sequences of an endogenous retrovirus and the entire circular genome of a novel hepadnavirus. Giant Guitarfish, a rajiform elasmobranch listed as ‘vulnerable’ on the IUCN Red List, are found in the tropical Western Indian Ocean. Proliferative skin lesions were observed on the ventrum and caudal fin of a juvenile male quarantined at a public aquarium following international shipment. Histologically, lesions consisted of papillomatous epidermal hyperplasia with myriad large, amphophilic, intranuclear inclusions. Deep sequencing and metagenomic analysis produced the complete genomes of two novel DNA viruses, a typical polyomavirus and a second unclassified virus with a 20 kb genome tentatively named Colossomavirus.
    [Show full text]
  • Metagenomic Identification of Diverse Animal Hepaciviruses and Pegiviruses
    bioRxiv preprint doi: https://doi.org/10.1101/2020.05.16.100149; this version posted May 17, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Metagenomic identification of diverse animal hepaciviruses and 2 pegiviruses 3 4 5 Ashleigh F. Porter1, John H.-O. Pettersson1,2, Wei-Shan Chang1, Erin Harvey1, Karrie Rose3, 6 Mang Shi5, John-Sebastian Eden1,4, Jan Buchmann1, Craig Moritz6, Edward C. Holmes1 7 8 9 1. Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and 10 Environmental Sciences and School of Medical Sciences, The University of Sydney, 11 Sydney, Australia. 12 2. Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, 13 Uppsala University, Uppsala, Sweden. 14 3. Australian Registry of Wildlife Health, Taronga Conservation Society Australia, 15 Mosman, Australia. 16 4. Centre for Virus Research, Westmead Institute for Medical Research, Westmead, 17 Australia. 18 5. School of Medicine, Sun Yat-sen University, Guangzhou, China. 19 6. Research School of Biology, and Centre for Biodiversity Analysis, Australian National 20 University, Acton, ACT, Australia. 21 22 23 Address correspondence to: 24 Edward C. Holmes, 25 Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and 26 Environmental Sciences and School of Medical Sciences, The University of Sydney, 27 Sydney, Australia 28 [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.05.16.100149; this version posted May 17, 2020.
    [Show full text]
  • Viruses in Transplantation - Not Always Enemies
    Viruses in transplantation - not always enemies Virome and transplantation ECCMID 2018 - Madrid Prof. Laurent Kaiser Head Division of Infectious Diseases Laboratory of Virology Geneva Center for Emerging Viral Diseases University Hospital of Geneva ESCMID eLibrary © by author Conflict of interest None ESCMID eLibrary © by author The human virome: definition? Repertoire of viruses found on the surface of/inside any body fluid/tissue • Eukaryotic DNA and RNA viruses • Prokaryotic DNA and RNA viruses (phages) 25 • The “main” viral community (up to 10 bacteriophages in humans) Haynes M. 2011, Metagenomic of the human body • Endogenous viral elements integrated into host chromosomes (8% of the human genome) • NGS is shaping the definition Rascovan N et al. Annu Rev Microbiol 2016;70:125-41 Popgeorgiev N et al. Intervirology 2013;56:395-412 Norman JM et al. Cell 2015;160:447-60 ESCMID eLibraryFoxman EF et al. Nat Rev Microbiol 2011;9:254-64 © by author Viruses routinely known to cause diseases (non exhaustive) Upper resp./oropharyngeal HSV 1 Influenza CNS Mumps virus Rhinovirus JC virus RSV Eye Herpes viruses Parainfluenza HSV Measles Coronavirus Adenovirus LCM virus Cytomegalovirus Flaviviruses Rabies HHV6 Poliovirus Heart Lower respiratory HTLV-1 Coxsackie B virus Rhinoviruses Parainfluenza virus HIV Coronaviruses Respiratory syncytial virus Parainfluenza virus Adenovirus Respiratory syncytial virus Coronaviruses Gastro-intestinal Influenza virus type A and B Human Bocavirus 1 Adenovirus Hepatitis virus type A, B, C, D, E Those that cause
    [Show full text]
  • Diversity and Evolution of Viral Pathogen Community in Cave Nectar Bats (Eonycteris Spelaea)
    viruses Article Diversity and Evolution of Viral Pathogen Community in Cave Nectar Bats (Eonycteris spelaea) Ian H Mendenhall 1,* , Dolyce Low Hong Wen 1,2, Jayanthi Jayakumar 1, Vithiagaran Gunalan 3, Linfa Wang 1 , Sebastian Mauer-Stroh 3,4 , Yvonne C.F. Su 1 and Gavin J.D. Smith 1,5,6 1 Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; [email protected] (D.L.H.W.); [email protected] (J.J.); [email protected] (L.W.); [email protected] (Y.C.F.S.) [email protected] (G.J.D.S.) 2 NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore 119077, Singapore 3 Bioinformatics Institute, Agency for Science, Technology and Research, Singapore 138671, Singapore; [email protected] (V.G.); [email protected] (S.M.-S.) 4 Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore 5 SingHealth Duke-NUS Global Health Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore 168753, Singapore 6 Duke Global Health Institute, Duke University, Durham, NC 27710, USA * Correspondence: [email protected] Received: 30 January 2019; Accepted: 7 March 2019; Published: 12 March 2019 Abstract: Bats are unique mammals, exhibit distinctive life history traits and have unique immunological approaches to suppression of viral diseases upon infection. High-throughput next-generation sequencing has been used in characterizing the virome of different bat species. The cave nectar bat, Eonycteris spelaea, has a broad geographical range across Southeast Asia, India and southern China, however, little is known about their involvement in virus transmission.
    [Show full text]